Multiple Sequence Alignment

The goal of this section is to compare and evaluate the robustness of several multiple sequence alignment programs. As test-dataset Rieske iron sulfur protein sequences from a number of species are used. The critical functional site of this protein family bind an iron-sulfur $[\text{Fe}_2\text{S}_2]$ cluster with the two known consensus amino acid binding motifs CXHXGC and CXXH. Investigate, in particular, the ability of the multiple sequence alignment programs to discover the two conserved binding motifs as well as to correctly align the rest of the protein sequences.

        

1. Download the protein sequences with the following accession numbers in FASTA format from NCBI Entrez database: P08067, P20788, AAD55565, P08980, P23136, AAC84018, AAF02198.
2. Use the progressive alignment program ClustalW
   http://www.ch.embnet.org/software/ClustalW.html to align the sequences. (Save resulting multiple alignment in ClustalW format).
3. Check the quality of the alignment visually and by using the alignment quality evaluation web service CORE
   http://igs-server.cnrs-mrs.fr/Tcoffee/tcoffee_cgi/index.cgi.
4. Use the profile-based alignment program MultiAlign
   http://bioinfo.genotoul.fr/multalin/ to align the sequences. (Note: conversions between different file formats can be done by the program Readseq
   http://iubio.bio.indiana.edu/cgi-bin/readseq.cgi. Use CORE to check the quality of the multiple alignment).
5. Use the semi-exhaustive program DCA
   http://bibiserv.techfak.uni-bielefeld.de/dca/submission.html to align the sequences. (Do a quality evaluation as above).
6. Use the iterative tree-based program PRRN http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/cgi-bin/prrn.pl to align the sequences. (Do a quality evaluation as above).
7. Finally use the program T-Coffee
   http://igs-server.cnrs-mrs.fr/Tcoffee/tcoffee_cgi/index.cgi to align the sequences. (Do a quality evaluation as above).
8. Carefully compare the results from the different methods. Can you identify the most reasonable alignment? Which method appears to be the best?